Problem with alternator

My son just bought a 2003 v6 mustang. When he got the car the battery kept dying. We found out that the previous owner left the underdrive pulleys on and it wouldnt charge properly. The dealer put in a new alternator, battery and pulleys. The upper pulley is a little larger than the stock one. We have a 2002 mustang also and there is about a 1/2 more space between the pulleys than the 03.
Now the car isn't charging properly again. Sometimes it charges and sometimes it wont. Resulting in the car stalling, accesories not working etc. This is an intermittent problem.

My question is this. Can the oversized pulley damage a new stock alternator ? What should I do at this point. I had the alt. checked and it comes and goes.

Should I change the pulleys or put in a performance alt? Any help would be greatly appreciated, its the kids first car and hes pretty bummed. Also I live in North Jersey. Does anyone know a good stang mechanic in these parts.

Thanks